# MMalign.pdb # **************************************************************************** DSSR: Software for Defining the (Secondary) Structures of RNA by Xiang-Jun Lu (xiangjun@x3dna.org), beta-r08-on-20130323 The program is currently under active development. As always, we greatly appreciate your feedback! Please report all DSSR-related issues on the 3DNA Forum (http://forum.x3dna.org/), and I strive to promptly respond to any questions posted there. **************************************************************************** Date and time: Wed May 10 06:23:45 2023 File name: MMalign.pdb no. of DNA/RNA chains: 1 [C=111] no. of nucleotides: 111 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 63 base pair(s) 1 C.G1 C.C111 [G-C] WC 19-XIX cWW cW-W -177.7(anti) C3'-endo lambda=61.0; -157.1(anti) C3'-endo lambda=64.7 d(C1'-C1')=10.28 d(N1-N9)=8.84 d(C6-C8)=10.05 tor(N1-C1'-C1'-N9)=34.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.44]; N1(imino)-N3[2.96]; N2(amino)-O2(carbonyl)[2.38]" bp_pars: [0.05 0.08 -0.39 4.19 -2.39 12.61] 2 C.G2 C.C110 [G-C] WC 19-XIX cWW cW-W -157.1(anti) C3'-endo lambda=61.0; -163.7(anti) C3'-endo lambda=61.3 d(C1'-C1')=10.39 d(N1-N9)=8.92 d(C6-C8)=10.03 tor(N1-C1'-C1'-N9)=2.7 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.29]; N1(imino)-N3[2.96]; N2(amino)-O2(carbonyl)[2.51]" bp_pars: [-0.27 0.03 -0.03 -3.95 -4.91 8.16] 3 C.A3 C.U109 [A-U] WC 20-XX cWW cW-W -175.4(anti) C3'-endo lambda=50.7; -171.9(anti) C3'-endo lambda=49.0 d(C1'-C1')=11.23 d(N1-N9)=9.15 d(C6-C8)=9.93 tor(N1-C1'-C1'-N9)=-23.0 H-bonds[2]: "N6(amino)-O4(carbonyl)[2.85]; N1-N3(imino)[2.99]" bp_pars: [0.37 -0.01 -0.39 -0.87 10.91 -7.63] 4 C.C4 C.G108 [C-G] WC 19-XIX cWW cW-W -157.2(anti) C3'-endo lambda=54.0; -163.4(anti) C3'-endo lambda=64.7 d(C1'-C1')=10.30 d(N1-N9)=8.81 d(C6-C8)=9.96 tor(N1-C1'-C1'-N9)=-20.7 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.45]; N3-N1(imino)[2.89]; N3-N2(amino)[2.83]" bp_pars: [-0.41 -0.02 0.63 10.14 -30.10 9.72] 5 C.C5 C.G107 [C-G] WC 19-XIX cWW cW-W -171.4(anti) C3'-endo lambda=62.0; -161.1(anti) C3'-endo lambda=55.2 d(C1'-C1')=10.28 d(N1-N9)=8.81 d(C6-C8)=9.91 tor(N1-C1'-C1'-N9)=-7.1 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.52]; N3-N1(imino)[2.87]; N4(amino)-O6(carbonyl)[3.22]" bp_pars: [0.38 -0.09 0.05 -5.30 -13.02 8.19] 6 C.U6 C.A106 [U-A] WC 20-XX cWW cW-W -163.2(anti) C3'-endo lambda=49.9; -150.2(anti) C3'-exo lambda=61.2 d(C1'-C1')=10.84 d(N1-N9)=9.36 d(C6-C8)=10.33 tor(N1-C1'-C1'-N9)=40.4 H-bonds[2]: "N3(imino)-N1[3.43]; O4(carbonyl)-N6(amino)[3.48]" bp_pars: [-0.11 0.35 -0.89 -4.08 -12.92 2.51] 7 C.C7 C.G105 [C-G] WC 19-XIX cWW cW-W -159.6(anti) C3'-endo lambda=54.6; -176.0(anti) C3'-endo lambda=46.9 d(C1'-C1')=11.50 d(N1-N9)=9.70 d(C6-C8)=10.66 tor(N1-C1'-C1'-N9)=-8.8 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.55]; N3-N1(imino)[3.74]; N4(amino)-O6(carbonyl)[3.82]" bp_pars: [0.82 0.61 -0.10 3.21 -4.43 1.84] 8 C.G8 C.C104 [G-C] WC 19-XIX cWW cW-W -159.7(anti) C3'-endo lambda=55.4; -168.4(anti) C3'-endo lambda=53.3 d(C1'-C1')=10.81 d(N1-N9)=9.17 d(C6-C8)=10.20 tor(N1-C1'-C1'-N9)=0.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.36]; N1(imino)-N3[3.18]; N2(amino)-O2(carbonyl)[2.86]" bp_pars: [-0.34 0.19 -0.07 -6.09 0.94 4.63] 9 C.C9 C.G103 [C-G] WC 19-XIX cWW cW-W -161.8(anti) C3'-endo lambda=55.3; -161.4(anti) C3'-endo lambda=59.8 d(C1'-C1')=10.74 d(N1-N9)=9.14 d(C6-C8)=10.22 tor(N1-C1'-C1'-N9)=-16.2 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.74]; N3-N1(imino)[3.15]; N4(amino)-O6(carbonyl)[3.46]" bp_pars: [-0.00 0.22 0.29 4.92 -9.02 6.83] 10 C.A10 C.U102 [A-U] WC 20-XX cWW cW-W -131.4(anti) C2'-endo lambda=57.0; 179.5(anti) C3'-endo lambda=53.8 d(C1'-C1')=11.14 d(N1-N9)=9.34 d(C6-C8)=10.24 tor(N1-C1'-C1'-N9)=24.3 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.51]; N1-N3(imino)[3.48]" bp_pars: [-0.39 0.47 -0.25 22.13 4.70 -1.18] 11 C.A11 C.U102 [A-U] 00-n/a cWW cW-W -151.4(anti) C3'-endo lambda=76.7; 179.5(anti) C3'-endo lambda=71.7 d(C1'-C1')=8.50 d(N1-N9)=7.62 d(C6-C8)=9.09 tor(N1-C1'-C1'-N9)=-9.7 H-bonds[1]: "N1-N3(imino)[2.48]" bp_pars: [0.07 -0.28 1.79 34.12 -9.08 27.74] 12 C.G13 C.C60 [G+C] 00-n/a cWH cW+M -177.9(anti) C3'-endo lambda=55.5; -161.9(anti) C3'-endo lambda=38.9 d(C1'-C1')=11.50 d(N1-N9)=9.45 d(C6-C8)=8.81 tor(N1-C1'-C1'-N9)=-8.8 H-bonds[2]: "O6(carbonyl)-N4(amino)[2.87]; N2(amino)-OP2[3.34]" bp_pars: [0.47 4.84 0.35 -8.67 -6.49 -87.18] 13 C.G14 C.C61 [G+C] 00-n/a cWH cW+M -165.5(anti) C3'-endo lambda=55.6; -161.2(anti) C3'-endo lambda=41.8 d(C1'-C1')=11.29 d(N1-N9)=9.22 d(C6-C8)=8.59 tor(N1-C1'-C1'-N9)=-18.5 H-bonds[2]: "O6(carbonyl)-N4(amino)[2.83]; N2(amino)-OP2[2.79]" bp_pars: [0.46 4.70 0.77 -11.94 -11.20 -84.86] 14 C.U15 C.C18 [U-C] 00-n/a tWH cW-M -115.5(anti) C3'-exo lambda=46.3; -161.3(anti) C3'-endo lambda=26.0 d(C1'-C1')=9.64 d(N1-N9)=7.46 d(C6-C8)=6.39 tor(N1-C1'-C1'-N9)=-60.6 H-bonds[1]: "O2(carbonyl)-N4(amino)[2.97]" bp_pars: [3.08 -0.48 -1.75 30.91 16.50 -116.49] 15 C.A16 C.A65 [A-A] 00-n/a ... c... -163.9(anti) C3'-endo lambda=41.0; -159.0(anti) C3'-endo lambda=39.0 d(C1'-C1')=13.30 d(N1-N9)=10.88 d(C6-C8)=10.84 tor(N1-C1'-C1'-N9)=-4.6 H-bonds[1]: "N6(amino)*N6(amino)[2.49]" bp_pars: [0.48 1.31 -2.05 -0.42 -33.81 -30.44] 16 C.A16 C.U66 [A-U] WC 20-XX cWW cW-W -163.9(anti) C3'-endo lambda=59.9; -154.8(anti) C3'-endo lambda=67.8 d(C1'-C1')=10.00 d(N1-N9)=8.62 d(C6-C8)=9.88 tor(N1-C1'-C1'-N9)=-18.9 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.69]; N1-N3(imino)[2.93]" bp_pars: [-0.61 -0.03 0.84 1.44 -15.56 13.92] 17 C.U17 C.A65 [U-A] 00-n/a cWW cW-W -152.7(anti) C3'-endo lambda=68.9; -159.0(anti) C3'-endo lambda=54.9 d(C1'-C1')=10.44 d(N1-N9)=9.04 d(C6-C8)=10.24 tor(N1-C1'-C1'-N9)=-25.1 H-bonds[2]: "O2(carbonyl)*N1[3.18]; N3(imino)-N1[3.42]" bp_pars: [1.07 0.23 1.28 -6.53 -34.19 9.87] 18 C.C18 C.G64 [C-G] WC 19-XIX cWW cW-W -161.3(anti) C3'-endo lambda=53.7; -178.8(anti) C3'-endo lambda=55.1 d(C1'-C1')=11.20 d(N1-N9)=9.50 d(C6-C8)=10.41 tor(N1-C1'-C1'-N9)=-9.7 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.47]; N3-N1(imino)[3.62]; N4(amino)-O6(carbonyl)[3.66]" bp_pars: [0.03 0.47 0.91 18.57 -7.93 -0.75] 19 C.A19 C.U63 [A-U] WC 20-XX cWW cW-W -156.5(anti) C3'-endo lambda=56.0; -162.7(anti) C3'-endo lambda=53.4 d(C1'-C1')=10.60 d(N1-N9)=8.96 d(C6-C8)=9.97 tor(N1-C1'-C1'-N9)=-16.5 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.39]; N1-N3(imino)[2.99]" bp_pars: [-0.06 0.05 0.64 11.33 -25.59 2.20] 20 C.U20 C.G62 [U-G] 00-n/a cWW cW-W -168.3(anti) C3'-endo lambda=68.0; -168.1(anti) C3'-endo lambda=56.0 d(C1'-C1')=10.79 d(N1-N9)=9.38 d(C6-C8)=10.64 tor(N1-C1'-C1'-N9)=-15.3 H-bonds[1]: "O2(carbonyl)-N2(amino)[2.92]" bp_pars: [0.76 0.68 0.34 1.65 -19.11 14.04] 21 C.G21 C.C61 [G-C] WC 19-XIX cWW cW-W 178.9(anti) C3'-endo lambda=53.6; -161.2(anti) C3'-endo lambda=60.3 d(C1'-C1')=10.67 d(N1-N9)=9.13 d(C6-C8)=10.21 tor(N1-C1'-C1'-N9)=-1.4 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.52]; N1(imino)-N3[3.23]; N2(amino)-O2(carbonyl)[2.83]" bp_pars: [-0.74 0.18 0.00 1.40 -4.70 7.29] 22 C.G22 C.C60 [G-C] WC 19-XIX cWW cW-W -163.7(anti) C3'-endo lambda=62.9; -161.9(anti) C3'-endo lambda=58.8 d(C1'-C1')=10.66 d(N1-N9)=9.18 d(C6-C8)=10.31 tor(N1-C1'-C1'-N9)=-5.4 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.69]; N1(imino)-N3[3.24]; N2(amino)-O2(carbonyl)[2.74]" bp_pars: [-0.04 0.31 0.55 -4.97 -13.38 8.66] 23 C.C23 C.G59 [C-G] WC 19-XIX cWW cW-W -164.4(anti) C3'-endo lambda=49.5; -165.4(anti) C3'-endo lambda=48.3 d(C1'-C1')=11.26 d(N1-N9)=9.42 d(C6-C8)=10.28 tor(N1-C1'-C1'-N9)=-21.7 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.36]; N3-N1(imino)[3.28]; N4(amino)-O6(carbonyl)[3.30]" bp_pars: [-0.06 0.25 0.37 -1.78 -21.00 -3.59] 24 C.G24 C.C58 [G-C] WC 19-XIX cWW cW-W -162.4(anti) C3'-endo lambda=63.5; -158.7(anti) C3'-endo lambda=61.8 d(C1'-C1')=10.63 d(N1-N9)=9.26 d(C6-C8)=10.45 tor(N1-C1'-C1'-N9)=4.7 H-bonds[4]: "O6(carbonyl)-N4(amino)[3.80]; N1(imino)-N3[3.33]; N2(amino)-O2(carbonyl)[2.75]; N2(amino)-N3[3.25]" bp_pars: [0.36 0.47 0.11 2.42 -4.83 11.83] 25 C.G25 C.C57 [G-C] WC 19-XIX cWW cW-W -163.3(anti) C3'-endo lambda=56.4; -163.3(anti) C3'-endo lambda=56.8 d(C1'-C1')=10.78 d(N1-N9)=9.13 d(C6-C8)=10.22 tor(N1-C1'-C1'-N9)=-8.5 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.44]; N1(imino)-N3[3.19]; N2(amino)-O2(carbonyl)[2.88]" bp_pars: [0.09 0.22 -0.44 7.74 -8.21 7.63] 26 C.A26 C.U56 [A-U] WC 20-XX cWW cW-W -164.9(anti) C3'-endo lambda=60.1; -152.0(anti) C3'-endo lambda=57.3 d(C1'-C1')=10.17 d(N1-N9)=8.67 d(C6-C8)=9.77 tor(N1-C1'-C1'-N9)=-13.6 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.32]; N1-N3(imino)[2.74]" bp_pars: [0.26 -0.18 0.66 -4.93 -24.73 5.91] 27 C.C27 C.G55 [C-G] WC 19-XIX cWW cW-W -157.5(anti) C3'-endo lambda=54.1; -164.8(anti) C3'-endo lambda=59.5 d(C1'-C1')=10.37 d(N1-N9)=8.76 d(C6-C8)=9.83 tor(N1-C1'-C1'-N9)=-10.2 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.41]; N3-N1(imino)[2.77]; N4(amino)-O6(carbonyl)[3.01]" bp_pars: [-0.30 -0.20 0.56 -3.35 2.20 6.47] 28 C.G28 C.C54 [G-C] WC 19-XIX cWW cW-W -169.8(anti) C3'-endo lambda=60.1; -164.1(anti) C3'-endo lambda=52.6 d(C1'-C1')=10.71 d(N1-N9)=9.10 d(C6-C8)=10.15 tor(N1-C1'-C1'-N9)=-0.7 H-bonds[4]: "O6(carbonyl)-N4(amino)[3.32]; N1(imino)-N3[3.09]; N2(amino)-O2(carbonyl)[2.75]; N2(amino)-N3[3.08]" bp_pars: [0.60 0.15 -0.26 -9.12 3.92 5.58] 29 C.A29 C.C53 [A-C] 00-n/a ... c... -167.1(anti) C3'-endo lambda=50.5; -158.2(anti) C3'-endo lambda=57.5 d(C1'-C1')=10.47 d(N1-N9)=8.79 d(C6-C8)=9.74 tor(N1-C1'-C1'-N9)=0.3 H-bonds[2]: "N6(amino)*N4(amino)[2.83]; N1*N3[2.69]" bp_pars: [-0.25 -0.22 0.23 -1.00 -4.92 1.46] 30 C.C30 C.G52 [C-G] WC 19-XIX cWW cW-W -172.3(anti) C3'-endo lambda=46.4; 180.0(anti) C3'-endo lambda=43.9 d(C1'-C1')=11.11 d(N1-N9)=9.19 d(C6-C8)=10.16 tor(N1-C1'-C1'-N9)=-15.4 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.90]; N3-N1(imino)[3.10]; N4(amino)-O6(carbonyl)[3.17]" bp_pars: [-0.25 0.13 -0.22 4.90 3.03 1.63] 31 C.C31 C.G51 [C-G] WC 19-XIX cWW cW-W -170.1(anti) C3'-endo lambda=48.0; -171.8(anti) C3'-endo lambda=55.3 d(C1'-C1')=10.55 d(N1-N9)=8.80 d(C6-C8)=9.77 tor(N1-C1'-C1'-N9)=-0.8 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.62]; N3-N1(imino)[2.78]; N4(amino)-O6(carbonyl)[2.85]" bp_pars: [-0.22 -0.24 -0.78 11.43 -8.79 3.18] 32 C.G32 C.C50 [G-C] WC 19-XIX cWW cW-W -166.1(anti) C3'-endo lambda=57.9; -160.9(anti) C3'-endo lambda=58.3 d(C1'-C1')=10.59 d(N1-N9)=9.04 d(C6-C8)=10.13 tor(N1-C1'-C1'-N9)=-2.7 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.34]; N1(imino)-N3[3.06]; N2(amino)-O2(carbonyl)[2.76]" bp_pars: [-0.03 0.12 -0.29 -0.36 -13.54 7.86] 33 C.G33 C.C49 [G-C] WC 19-XIX cWW cW-W -161.2(anti) C3'-endo lambda=62.1; -171.1(anti) C3'-endo lambda=52.6 d(C1'-C1')=10.72 d(N1-N9)=9.14 d(C6-C8)=10.18 tor(N1-C1'-C1'-N9)=-3.1 H-bonds[4]: "O6(carbonyl)-N4(amino)[3.29]; N1(imino)-N3[3.12]; N2(amino)-O2(carbonyl)[2.83]; N2(amino)-N3[3.15]" bp_pars: [0.58 0.14 -0.33 -0.06 -5.55 5.07] 34 C.G34 C.U48 [G-U] 00-n/a cWW cW-W -145.7(anti) C2'-endo lambda=43.9; -160.5(anti) C3'-endo lambda=56.1 d(C1'-C1')=10.84 d(N1-N9)=9.17 d(C6-C8)=10.07 tor(N1-C1'-C1'-N9)=25.9 H-bonds[3]: "O6(carbonyl)*O4(carbonyl)[3.20]; N1(imino)*N3(imino)[3.26]; N2(amino)-O2(carbonyl)[3.08]" bp_pars: [-0.56 0.06 0.08 -7.16 -7.62 -2.41] 35 C.U35 C.A47 [U-A] WC 20-XX cWW cW-W -166.9(anti) C3'-endo lambda=56.0; -156.0(anti) C3'-endo lambda=55.2 d(C1'-C1')=10.83 d(N1-N9)=9.16 d(C6-C8)=10.23 tor(N1-C1'-C1'-N9)=-14.4 H-bonds[2]: "N3(imino)-N1[3.22]; O4(carbonyl)-N6(amino)[3.51]" bp_pars: [0.21 0.30 -0.12 -4.45 -8.83 5.62] 36 C.U36 C.G46 [U-G] Wobble 28-XXVIII cWW cW-W -154.6(anti) C3'-endo lambda=70.9; -171.4(anti) C3'-endo lambda=52.4 d(C1'-C1')=10.30 d(N1-N9)=8.90 d(C6-C8)=10.03 tor(N1-C1'-C1'-N9)=-15.7 H-bonds[3]: "O2(carbonyl)-N1(imino)[2.80]; O2(carbonyl)-N2(amino)[3.18]; N3(imino)-O6(carbonyl)[3.39]" bp_pars: [2.07 -0.18 0.78 -4.91 -25.90 8.92] 37 C.C37 C.G45 [C-G] WC 19-XIX cWW cW-W -159.5(anti) C3'-endo lambda=50.5; -153.5(anti) C2'-exo lambda=59.9 d(C1'-C1')=10.13 d(N1-N9)=8.55 d(C6-C8)=9.35 tor(N1-C1'-C1'-N9)=7.9 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.87]; N3-N1(imino)[2.45]; N4(amino)-O6(carbonyl)[2.59]" bp_pars: [0.30 -0.67 0.22 1.66 -34.22 -5.44] 38 C.G38 C.A40 [G+A] 00-n/a cSH cm+M -161.7(anti) C3'-endo lambda=116.1; -164.8(anti) C3'-endo lambda=17.1 d(C1'-C1')=9.41 d(N1-N9)=8.80 d(C6-C8)=9.05 tor(N1-C1'-C1'-N9)=-21.1 H-bonds[2]: "N2(amino)*N6(amino)[2.48]; N3-N6(amino)[3.12]" bp_pars: [5.78 -1.15 1.86 -49.12 -18.77 -35.67] 39 C.G38 C.C43 [G-C] WC 19-XIX cWW cW-W -161.7(anti) C3'-endo lambda=42.1; -95.2(anti) C2'-endo lambda=42.0 d(C1'-C1')=11.07 d(N1-N9)=8.92 d(C6-C8)=9.67 tor(N1-C1'-C1'-N9)=37.2 H-bonds[4]: "O6(carbonyl)*N3[2.82]; O6(carbonyl)-N4(amino)[3.07]; N1(imino)-O2(carbonyl)[3.16]; N1(imino)-N3[3.32]" bp_pars: [-1.60 -0.48 -0.74 -6.15 -6.62 -6.49] 40 C.G38 C.C44 [G-C] 00-n/a cWW cW-W -161.7(anti) C3'-endo lambda=64.1; -153.9(anti) C3'-endo lambda=62.4 d(C1'-C1')=9.97 d(N1-N9)=8.61 d(C6-C8)=9.83 tor(N1-C1'-C1'-N9)=-9.6 H-bonds[2]: "O6(carbonyl)-N4(amino)[3.67]; N1(imino)-N3[2.86]" bp_pars: [-0.03 -0.08 0.90 -15.33 -26.03 12.27] 41 C.A39 C.G45 [A-G] 11-XI tHS cM-m 174.9(anti) C3'-endo lambda=20.9; -153.5(anti) C2'-exo lambda=114.0 d(C1'-C1')=8.93 d(N1-N9)=8.24 d(C6-C8)=8.89 tor(N1-C1'-C1'-N9)=63.6 H-bonds[3]: "N7-N2(amino)[3.85]; N6(amino)-O2'(hydroxyl)[2.76]; N6(amino)-N3[3.19]" bp_pars: [-6.96 -4.25 -0.44 16.14 -12.26 17.33] 42 C.A40 C.C44 [A-C] 00-n/a cWS cW-m -164.8(anti) C3'-endo lambda=46.4; -153.9(anti) C3'-endo lambda=116.2 d(C1'-C1')=9.63 d(N1-N9)=9.29 d(C6-C8)=10.79 tor(N1-C1'-C1'-N9)=17.4 H-bonds[1]: "N6(amino)-O2(carbonyl)[3.77]" bp_pars: [-5.70 0.26 -2.09 23.82 4.52 51.36] 43 C.A40 C.G45 [A-G] 00-n/a c.S c.-m -164.8(anti) C3'-endo lambda=33.7; -153.5(anti) C2'-exo lambda=124.0 d(C1'-C1')=8.40 d(N1-N9)=7.98 d(C6-C8)=9.25 tor(N1-C1'-C1'-N9)=34.0 H-bonds[2]: "N6(amino)-N3[3.07]; N1*O4'[2.87]" bp_pars: [-6.85 -1.77 1.04 17.58 -0.92 71.10] 44 C.C41 C.C44 [C-C] 00-n/a ... c... -144.4(anti) C3'-endo lambda=64.5; -153.9(anti) C3'-endo lambda=128.5 d(C1'-C1')=5.74 d(N1-N9)=6.03 d(C6-C8)=8.18 tor(N1-C1'-C1'-N9)=13.6 H-bonds[2]: "O2(carbonyl)-O2'(hydroxyl)[3.06]; N3*O2(carbonyl)[2.84]" bp_pars: [-3.05 1.55 -1.25 44.97 12.60 98.47] 45 C.C42 C.C44 [C-C] 00-n/a cWS cW-m -159.7(anti) C3'-endo lambda=66.9; -153.9(anti) C3'-endo lambda=106.8 d(C1'-C1')=3.64 d(N1-N9)=3.74 d(C6-C8)=5.66 tor(N1-C1'-C1'-N9)=58.6 H-bonds[1]: "N4(amino)-O2(carbonyl)[3.30]" bp_pars: [-2.20 0.85 0.31 40.15 21.27 129.32] 46 C.C67 C.G99 [C-G] WC 19-XIX cWW cW-W -147.3(anti) C3'-endo lambda=60.4; -136.9(anti) C1'-exo lambda=63.3 d(C1'-C1')=10.44 d(N1-N9)=9.02 d(C6-C8)=10.11 tor(N1-C1'-C1'-N9)=17.9 H-bonds[4]: "O2(carbonyl)-N2(amino)[2.69]; N3-N1(imino)[3.05]; N3-N2(amino)[3.27]; N4(amino)-O6(carbonyl)[3.31]" bp_pars: [-0.25 0.07 -0.67 1.81 -4.25 7.42] 47 C.C68 C.G98 [C-G] WC 19-XIX cWW cW-W -160.6(anti) C3'-endo lambda=55.4; -163.6(anti) C3'-endo lambda=57.1 d(C1'-C1')=10.86 d(N1-N9)=9.19 d(C6-C8)=10.13 tor(N1-C1'-C1'-N9)=-0.0 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.07]; N3-N1(imino)[3.16]; N4(amino)-O6(carbonyl)[3.15]" bp_pars: [0.14 0.09 -0.50 -2.61 -7.28 0.89] 48 C.A69 C.A97 [A-A] 00-n/a ... c... -153.6(anti) C3'-endo lambda=45.9; -160.7(anti) C3'-endo lambda=35.1 d(C1'-C1')=12.31 d(N1-N9)=10.16 d(C6-C8)=10.27 tor(N1-C1'-C1'-N9)=12.9 H-bonds[1]: "N6(amino)*N6(amino)[2.35]" bp_pars: [1.01 0.69 -1.51 -11.16 -5.76 -28.52] 49 C.U70 C.A97 [U-A] WC 20-XX cWW cW-W -167.6(anti) C3'-endo lambda=53.1; -160.7(anti) C3'-endo lambda=50.0 d(C1'-C1')=10.61 d(N1-N9)=8.86 d(C6-C8)=9.78 tor(N1-C1'-C1'-N9)=-29.3 H-bonds[2]: "N3(imino)-N1[2.98]; O4(carbonyl)-N6(amino)[3.32]" bp_pars: [0.35 -0.25 1.17 -0.55 -22.66 -3.59] 50 C.G71 C.C96 [G-C] WC 19-XIX cWW cW-W -161.5(anti) O4'-endo lambda=55.6; -163.5(anti) C3'-endo lambda=47.2 d(C1'-C1')=10.94 d(N1-N9)=9.13 d(C6-C8)=9.92 tor(N1-C1'-C1'-N9)=-6.8 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.80]; N1(imino)-N3[2.95]; N2(amino)-O2(carbonyl)[3.26]" bp_pars: [0.33 -0.09 -0.26 -8.31 -25.55 -5.00] 51 C.G73 C.C95 [G-C] WC 19-XIX cWW cW-W -157.1(anti) C3'-endo lambda=48.3; -160.6(anti) C3'-endo lambda=55.7 d(C1'-C1')=10.29 d(N1-N9)=8.55 d(C6-C8)=9.55 tor(N1-C1'-C1'-N9)=-0.1 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.86]; N1(imino)-N3[2.72]; N2(amino)-O2(carbonyl)[2.48]" bp_pars: [-0.83 -0.48 -0.28 9.59 1.20 3.53] 52 C.G74 C.A93 [G-A] Imino 08-VIII cWW cW-W -169.9(anti) C3'-endo lambda=41.3; -155.7(anti) C3'-endo lambda=44.0 d(C1'-C1')=13.38 d(N1-N9)=11.30 d(C6-C8)=11.60 tor(N1-C1'-C1'-N9)=8.0 H-bonds[1]: "O6(carbonyl)-N6(amino)[3.63]" bp_pars: [-0.50 1.67 -2.35 -2.38 -12.64 -18.85] 53 C.G74 C.C94 [G-C] WC 19-XIX cWW cW-W -169.9(anti) C3'-endo lambda=51.9; -169.3(anti) C3'-endo lambda=45.0 d(C1'-C1')=11.10 d(N1-N9)=9.29 d(C6-C8)=10.19 tor(N1-C1'-C1'-N9)=-13.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.16]; N1(imino)-N3[3.18]; N2(amino)-O2(carbonyl)[3.13]" bp_pars: [0.09 0.19 0.01 -8.89 -12.45 -1.42] 54 C.U75 C.A92 [U-A] 00-n/a cWW cW-W -159.9(anti) C3'-endo lambda=46.1; -151.1(anti) C3'-endo lambda=39.9 d(C1'-C1')=12.13 d(N1-N9)=10.01 d(C6-C8)=10.44 tor(N1-C1'-C1'-N9)=-10.4 H-bonds[1]: "O4(carbonyl)-N6(amino)[3.10]" bp_pars: [0.26 0.52 -1.69 1.28 -33.25 -16.99] 55 C.U75 C.A93 [U-A] WC 20-XX cWW cW-W -159.9(anti) C3'-endo lambda=63.2; -155.7(anti) C3'-endo lambda=59.3 d(C1'-C1')=10.09 d(N1-N9)=8.72 d(C6-C8)=10.01 tor(N1-C1'-C1'-N9)=-21.2 H-bonds[2]: "N3(imino)-N1[2.96]; O4(carbonyl)-N6(amino)[3.81]" bp_pars: [0.07 0.12 0.83 -1.53 -19.33 14.87] 56 C.U76 C.G91 [U-G] 00-n/a ... c... -159.4(anti) C3'-endo lambda=45.6; -167.5(anti) C3'-endo lambda=39.8 d(C1'-C1')=11.96 d(N1-N9)=9.86 d(C6-C8)=10.26 tor(N1-C1'-C1'-N9)=-3.7 H-bonds[1]: "O4(carbonyl)*O6(carbonyl)[3.02]" bp_pars: [0.29 0.42 -1.43 12.66 -10.24 -22.10] 57 C.U76 C.A92 [U-A] 00-n/a cWW cW-W -159.4(anti) C3'-endo lambda=63.1; -151.1(anti) C3'-endo lambda=62.9 d(C1'-C1')=9.13 d(N1-N9)=7.84 d(C6-C8)=9.21 tor(N1-C1'-C1'-N9)=-17.7 H-bonds[1]: "O4(carbonyl)-N6(amino)[3.14]" bp_pars: [-0.21 -0.61 0.65 1.40 -15.81 19.28] 58 C.A77 C.G88 [A-G] 00-n/a cWW cW-W -152.3(anti) C3'-endo lambda=36.8; -169.5(anti) C3'-endo lambda=41.6 d(C1'-C1')=12.94 d(N1-N9)=10.68 d(C6-C8)=10.58 tor(N1-C1'-C1'-N9)=6.6 H-bonds[1]: "N6(amino)-O6(carbonyl)[2.34]" bp_pars: [-0.94 1.09 -1.96 11.20 -34.29 -33.48] 59 C.A77 C.U89 [A-U] WC 20-XX cWW cW-W -152.3(anti) C3'-endo lambda=52.4; -160.0(anti) C3'-endo lambda=54.0 d(C1'-C1')=10.84 d(N1-N9)=9.11 d(C6-C8)=10.05 tor(N1-C1'-C1'-N9)=-12.3 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.33]; N1-N3(imino)[3.13]" bp_pars: [-0.42 0.08 0.48 2.80 -21.80 -1.05] 60 C.C78 C.G88 [C-G] WC 19-XIX cWW cW-W -159.1(anti) C3'-endo lambda=57.4; -169.5(anti) C3'-endo lambda=59.4 d(C1'-C1')=10.17 d(N1-N9)=8.64 d(C6-C8)=9.79 tor(N1-C1'-C1'-N9)=-12.8 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.25]; N3-N1(imino)[2.84]; N4(amino)-O6(carbonyl)[3.39]" bp_pars: [0.26 -0.12 0.63 16.02 -17.52 9.74] 61 C.C79 C.G86 [C-G] WC 19-XIX cWW cW-W -162.7(anti) C3'-endo lambda=35.4; -173.4(anti) C3'-endo lambda=48.4 d(C1'-C1')=11.96 d(N1-N9)=9.71 d(C6-C8)=10.43 tor(N1-C1'-C1'-N9)=-35.2 H-bonds[2]: "N3-N2(amino)[3.58]; N4(amino)-O6(carbonyl)[3.28]" bp_pars: [-1.09 0.46 -0.90 19.80 -18.05 -6.83] 62 C.G80 C.C85 [G-C] WC 19-XIX cWW cW-W -150.6(anti) C2'-exo lambda=54.7; -168.7(anti) C3'-endo lambda=63.7 d(C1'-C1')=10.40 d(N1-N9)=8.89 d(C6-C8)=9.96 tor(N1-C1'-C1'-N9)=-4.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.31]; N1(imino)-N3[3.05]; N2(amino)-O2(carbonyl)[2.81]" bp_pars: [-0.72 -0.03 -0.21 10.87 -12.22 7.53] 63 C.C81 C.G84 [C-G] WC 19-XIX cWW cW-W -162.8(anti) C3'-endo lambda=59.3; -116.4(anti) C3'-endo lambda=65.1 d(C1'-C1')=9.59 d(N1-N9)=8.28 d(C6-C8)=9.43 tor(N1-C1'-C1'-N9)=4.8 H-bonds[2]: "N3-N1(imino)[2.37]; N4(amino)-O6(carbonyl)[2.94]" bp_pars: [-0.13 -0.52 -0.73 12.76 16.85 9.78] **************************************************************************** List of 6 multiplet(s) 1 nts=3 C.G13+C.G22+C.C60 [GGC] 2 nts=3 C.G14+C.G21+C.C61 [GGC] 3 nts=3* C.U15+C.C18+C.G64 [UCG] 4 nts=3 C.C37+C.A39+C.G45 [CAG] 5 nts=3 C.G38+C.A40+C.C44 [GAC] 6 nts=3 C.G38+C.C42+C.C43 [GCC] **************************************************************************** List of 3 helices helix=1[1] bps=10 1 C.G1 C.C111 [G-C] WC 19-XIX cWW cW-W 2 C.G2 C.C110 [G-C] WC 19-XIX cWW cW-W 3 C.A3 C.U109 [A-U] WC 20-XX cWW cW-W 4 C.C4 C.G108 [C-G] WC 19-XIX cWW cW-W 5 C.C5 C.G107 [C-G] WC 19-XIX cWW cW-W 6 C.U6 C.A106 [U-A] WC 20-XX cWW cW-W 7 C.C7 C.G105 [C-G] WC 19-XIX cWW cW-W 8 C.G8 C.C104 [G-C] WC 19-XIX cWW cW-W 9 C.C9 C.G103 [C-G] WC 19-XIX cWW cW-W 10 C.A10 C.U102 [A-U] WC 20-XX cWW cW-W helix=2[7] bps=31 1 C.C43 C.G38 [C-G] WC 19-XIX cWW cW-W 2 C.G45 C.C37 [G-C] WC 19-XIX cWW cW-W 3 C.G46 C.U36 [G-U] Wobble 28-XXVIII cWW cW-W 4 C.A47 C.U35 [A-U] WC 20-XX cWW cW-W 5 C.U48 C.G34 [U-G] 00-n/a cWW cW-W 6 C.C49 C.G33 [C-G] WC 19-XIX cWW cW-W 7 C.C50 C.G32 [C-G] WC 19-XIX cWW cW-W 8 C.G51 C.C31 [G-C] WC 19-XIX cWW cW-W 9 C.G52 C.C30 [G-C] WC 19-XIX cWW cW-W 10 C.C53 C.A29 [C-A] 00-n/a ... c... 11 C.C54 C.G28 [C-G] WC 19-XIX cWW cW-W 12 C.G55 C.C27 [G-C] WC 19-XIX cWW cW-W 13 C.U56 C.A26 [U-A] WC 20-XX cWW cW-W 14 C.C57 C.G25 [C-G] WC 19-XIX cWW cW-W 15 C.C58 C.G24 [C-G] WC 19-XIX cWW cW-W 16 C.G59 C.C23 [G-C] WC 19-XIX cWW cW-W 17 C.C60 C.G22 [C-G] WC 19-XIX cWW cW-W 18 C.C61 C.G21 [C-G] WC 19-XIX cWW cW-W 19 C.G62 C.U20 [G-U] 00-n/a cWW cW-W 20 C.U63 C.A19 [U-A] WC 20-XX cWW cW-W 21 C.G64 C.C18 [G-C] WC 19-XIX cWW cW-W 22 C.A65 C.U17 [A-U] 00-n/a cWW cW-W 23 C.U66 C.A16 [U-A] WC 20-XX cWW cW-W 24 C.C67 C.G99 [C-G] WC 19-XIX cWW cW-W 25 C.C68 C.G98 [C-G] WC 19-XIX cWW cW-W 26 C.U70 C.A97 [U-A] WC 20-XX cWW cW-W 27 C.G71 C.C96 [G-C] WC 19-XIX cWW cW-W 28 C.G73 C.C95 [G-C] WC 19-XIX cWW cW-W 29 C.G74 C.C94 [G-C] WC 19-XIX cWW cW-W 30 C.U75 C.A93 [U-A] WC 20-XX cWW cW-W 31 C.U76 C.A92 [U-A] 00-n/a cWW cW-W helix=3[2] bps=5 1 C.A77 C.U89 [A-U] WC 20-XX cWW cW-W 2 C.C78 C.G88 [C-G] WC 19-XIX cWW cW-W 3 C.C79 C.G86 [C-G] WC 19-XIX cWW cW-W 4 C.G80 C.C85 [G-C] WC 19-XIX cWW cW-W 5 C.C81 C.G84 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 10 stems stem=1[#1] bps=10 1 C.G1 C.C111 [G-C] WC 19-XIX cWW cW-W 2 C.G2 C.C110 [G-C] WC 19-XIX cWW cW-W 3 C.A3 C.U109 [A-U] WC 20-XX cWW cW-W 4 C.C4 C.G108 [C-G] WC 19-XIX cWW cW-W 5 C.C5 C.G107 [C-G] WC 19-XIX cWW cW-W 6 C.U6 C.A106 [U-A] WC 20-XX cWW cW-W 7 C.C7 C.G105 [C-G] WC 19-XIX cWW cW-W 8 C.G8 C.C104 [G-C] WC 19-XIX cWW cW-W 9 C.C9 C.G103 [C-G] WC 19-XIX cWW cW-W 10 C.A10 C.U102 [A-U] WC 20-XX cWW cW-W stem=2[#2] bps=2 1 C.C18 C.G64 [C-G] WC 19-XIX cWW cW-W 2 C.A19 C.U63 [A-U] WC 20-XX cWW cW-W stem=3[#2] bps=8 1 C.G21 C.C61 [G-C] WC 19-XIX cWW cW-W 2 C.G22 C.C60 [G-C] WC 19-XIX cWW cW-W 3 C.C23 C.G59 [C-G] WC 19-XIX cWW cW-W 4 C.G24 C.C58 [G-C] WC 19-XIX cWW cW-W 5 C.G25 C.C57 [G-C] WC 19-XIX cWW cW-W 6 C.A26 C.U56 [A-U] WC 20-XX cWW cW-W 7 C.C27 C.G55 [C-G] WC 19-XIX cWW cW-W 8 C.G28 C.C54 [G-C] WC 19-XIX cWW cW-W stem=4[#2] bps=4 1 C.C30 C.G52 [C-G] WC 19-XIX cWW cW-W 2 C.C31 C.G51 [C-G] WC 19-XIX cWW cW-W 3 C.G32 C.C50 [G-C] WC 19-XIX cWW cW-W 4 C.G33 C.C49 [G-C] WC 19-XIX cWW cW-W stem=5[#2] bps=3 1 C.U35 C.A47 [U-A] WC 20-XX cWW cW-W 2 C.U36 C.G46 [U-G] Wobble 28-XXVIII cWW cW-W 3 C.C37 C.G45 [C-G] WC 19-XIX cWW cW-W stem=6[#2] bps=2 1 C.C67 C.G99 [C-G] WC 19-XIX cWW cW-W 2 C.C68 C.G98 [C-G] WC 19-XIX cWW cW-W stem=7[#2] bps=2 1 C.U70 C.A97 [U-A] WC 20-XX cWW cW-W 2 C.G71 C.C96 [G-C] WC 19-XIX cWW cW-W stem=8[#2] bps=3 1 C.G73 C.C95 [G-C] WC 19-XIX cWW cW-W 2 C.G74 C.C94 [G-C] WC 19-XIX cWW cW-W 3 C.U75 C.A93 [U-A] WC 20-XX cWW cW-W stem=9[#3] bps=2 1 C.A77 C.U89 [A-U] WC 20-XX cWW cW-W 2 C.C78 C.G88 [C-G] WC 19-XIX cWW cW-W stem=10[#3] bps=2 1 C.C79 C.G86 [C-G] WC 19-XIX cWW cW-W 2 C.G80 C.C85 [G-C] WC 19-XIX cWW cW-W **************************************************************************** List of 3 lone WC/wobble pair(s) -1 C.A16 C.U66 [A-U] WC 20-XX cWW cW-W -2 C.G38 C.C43 [G-C] WC 19-XIX cWW cW-W -3 C.C81 C.G84 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 2 coaxial stack(s) 1 Helix#2 contains 7 stems: [#2, #3, #4, #5, #6, #7, #8] 2 Helix#3 contains 2 stems: [#9, #10] **************************************************************************** List of 1 hairpin loop(s) 1 nts=4 AACC closed by pair {C.G38+C.C43 [GC], #-2} C.G38+C.A39+C.A40+C.C41+C.C42+C.C43 [GAACCC] **************************************************************************** List of 2 bulge(s) 1 bulge: 5 nts; [1x0]; linked by [#6, #7] C.C68+C.A69+C.U70+C.A97+C.G98 [CAUAG] 2 bulge: 5 nts; [1x0]; linked by [#7, #8] C.G71+C.C72+C.G73+C.C95+C.C96 [GCGCC] **************************************************************************** List of 5 internal loop(s) 1 symmetric internal loop: 6 nts; [1x1]; linked by [#-1, #2] C.A16+C.U17+C.C18+C.G64+C.A65+C.U66 [AUCGAU] 2 symmetric internal loop: 6 nts; [1x1]; linked by [#2, #3] C.A19+C.U20+C.G21+C.C61+C.G62+C.U63 [AUGCGU] 3 symmetric internal loop: 6 nts; [1x1]; linked by [#3, #4] C.G28+C.A29+C.C30+C.G52+C.C53+C.C54 [GACGCC] 4 symmetric internal loop: 6 nts; [1x1]; linked by [#4, #5] C.G33+C.G34+C.U35+C.A47+C.U48+C.C49 [GGUAUC] 5 asymmetric internal loop: 8 nts; [1x3]; linked by [#8, #9] C.U75+C.U76+C.A77+C.U89+C.C90+C.G91+C.A92+C.A93 [UUAUCGAA] **************************************************************************** >chain-C #1 RNA* with 111 nts GGACCUCGCAAGGGUAUCAUGGCGGACGACCGGGUUCGAACCCCGGAUCCGGCCGUCCGCCGUGAUCCAUGCGGUUACCGCCCGCGUGUCGAACCCAGGUGUGCGAGGUCC ((((((((((.....(.((.((((((((.((((.((((....).))).)))).)))))))).)).)((.((.(((.(((((..))).))...)))))))..)))))))))) DONE!